Changes
From Statistical Genetics Courses
/* Fine-mapping (SuSiE method) */
==Running Tutorials on Your Computer==
==Alohomora==
* [http://gmc.mdc-berlin.de/alohomora/ Software Link]
==AnnotationAnnovar complex traits==* [httphttps://statgengithub.uscom/filesstatgenetics/tutorials/functionalstatgen-annotationcourses/blob/master/handout/FunctionalAnnotation_exercise_2019FunctionalAnnotation.pdf Functional Annotation Exercise <nowiki>[PDF]</nowiki>]
* [[Commands in Annotation Exercise|Exercise Commands]]
To install run the exercise from packagesdocker image provided, follow the configuration steps above and run the following command.
<pre>sudo aptstatgen-setup login -get install annotation-tutorialannovar</pre>The exercise's files will then be installed in the folder ''/home/shared/functional_annotation''. You can run from there or copy the files into your user's home directory and proceed with the exercise.
==Annovar MEndelianMendelian traits==
* [http://statgen.us/files/tutorials/FunctionalAnnotation_Annovar_final.pdf Exercise <nowiki>[PDF]</nowiki>]
* [https://statgen.research.bcm.eduus/files/2017/09/commands/annovar-functional_annotation.txt Commands Part I - Functional Annotation]* [https://statgen.research.bcm.eduus/files/2017/09/commands/annovar-variant_filtering.txt Commands Part II - Variant Filtering]
==Cochran Armitage Trend Test==
* [httphttps://statgengithub.uscom/statgenetics/statgen-courses/blob/filesmaster/tutorialshandout/Armitage_sample_size_revisedArmitage_sample_size.pdf CATT Exercise <nowiki>[PDF]</nowiki>]
==Epistasis (PLINK and CASSI)==Result Files* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Epistasis_PLINK_CASSI.pdf Epistasis exercise <nowiki>[PDF]</nowiki>] To run the exercise from docker image provided, <pre>statgen-setup login --tutorial epistasis</pre> ==FastLMM==* [https://github.com/statgenetics/statgen-courses/blob/master/handout/FASTLMM.pdf FastLMM exercise <nowiki>[PDF]</nowiki>] To run the exercise from docker image provided, <pre>statgen-setup login --tutorial fastlmm-gcta</pre> ==Fine-mapping (SuSiE method)==* [httphttps://github.com/statgenetics/statgen-courses/blob/master/handout/finemapping.usdocx susieR Exercise <nowiki>[DOCX]</filesnowiki>]* [https:/2016/07github.com/gatk_resultsstatgenetics/statgen-courses/blob/master/handout/finemapping_answers.tardocx susieR Exercise Answers <nowiki>[DOCX]</nowiki>]* [https://github.gz GATKcom/IGV statgenetics/statgen-courses/blob/master/notebooks/finemapping.ipynb susieR Exercise <nowiki>[Ipython notebook]</nowiki>]* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/finemapping_answers.ipynb susieR Exercise Answers <nowiki>[Ipython notebook]</nowiki>] To run the exercisefrom docker image provided, <pre>statgen-setup launch --tutorial finemap</pre> ==GCTA==* [https://github.com/statgenetics/statgen-courses/blob/master/handout/GCTA.pdf GCTA exercise <nowiki>[PDF]</nowiki>] To run the exercise from docker image provided, <pre>statgen-setup login --tutorial fastlmm-gcta</pre>
==Gemini==
* [https://drive.googlegithub.com/filestatgenetics/dstatgen-courses/0B2pJ9cgevF3sTS1DeGxYalFTN00blob/view Bam files for master/handout/Gemini.docx Gemini exercise<nowiki>[DOCX]</nowiki>]
==Genehunter==
==GWAS: Data Quality Control==
* [httphttps://statgengithub.uscom/filesstatgenetics/tutorials/gwasstatgen-qccourses/blob/master/handout/PLINK_data_QC.pdf Exercise <nowiki>[PDF]</nowiki>]
* [[GWAS Data QC Exercise|Exercise Commands]]
==GWAS: Association Analysis Controlling for Population Substructure==
* [httphttps://statgengithub.uscom/filesstatgenetics/tutorials/gwasstatgen-substructurecourses/blob/master/handout/GWAS_Data_Controlling_for_Substructure_V2PLINK_Substructure.pdf Exercise <nowiki>[PDF]</nowiki>]
* [[GWAS_Controlling_for_Population_Substructure|Exercise Commands]]
<pre>sudo aptstatgen-setup login -get install plink-tutorialplink</pre>The exercise's ==Homozygosity Mapper==* [http://statgen.us/files will then be installed in the folder ''/hometutorials/Homozygosity_mapping_exercise_part_1.pdf Exercise Part I]* [http:/shared/Plink_substructure''statgen. You can run from there or copy the us/files into your user's home directory and proceed with the /tutorials/Homozygosity_mapping_exercise_part_2.pdf Exercise Part II]* [http://www.homozygositymapper.org Data Sets] ==IGV==* [https://github.com/statgenetics/statgen-courses/blob/master/handout/IGV.docx IGV exercise<nowiki>[DOCX]</nowiki>]* [http://statgen.us/files/igv_exercise.zip Exercise files (VCF and BAM)]
==Linkage/FastLinkage==
* [httphttps://github.com/statgenetics/statgen-courses/blob/master/handout/MLINK.uspdf LINKAGE Exercise <nowiki>[DOCX]</filesnowiki>] To run the exercise from docker image provided, <pre>statgen-setup login --tutorial mlink</tutorialspre> ==Pleiotropy==* [https:/SEQLinkage/linkage_intro_ex_berlin_2018_with_pg_numgithub.com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy.pdf Linkage Introduction Pleiotropy Exercise <nowiki>[PDF]</nowiki>]* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy_answers.pdf Pleiotropy Answers to Questions <nowiki>[PDF]</nowiki>] To run the exercise from docker image provided, <pre>statgen-setup login --tutorial pleiotropy</pre> ==Polygenic risk prediction (NPS method)==* [https://github.com/statgenetics/statgen-courses/blob/master/handout/NPS.pdf PRS NPS Exercise <nowiki>[DOCX]</nowiki>] To run the exercise from docker image provided, <pre>statgen-setup login --tutorial nps</pre> ==Polygenic risk prediction (LDpred2 method)==* [https://github.com/statgenetics/statgen-courses/blob/master/handout/ldpred2_example.pdf PRS LDpred2 Exercise <nowiki>[PDF]</nowiki>]* [https://github.com/cumc/bioworkflows/blob/master/ldpred/ldpred2_example.ipynb PRS LDpred2 Exercise <nowiki>[Ipython Notebook]</nowiki>] To run the exercise from docker image provided, <pre>statgen-setup launch --tutorial ldpred2</pre> Then follow prompts on the terminal output to open up the JupyterLab server in your web browser. If it is the first time you start this server, please open a command terminal inside JupyterLab, and type <pre>get-data</pre> to load the data-set to the JupyterLab workspace.
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==Population Genetics==
* [httphttps://statgengithub.uscom/filesstatgenetics/tutorialsstatgen-courses/populationblob/Popgen_exe_ansmaster/handout/PopGen.pdf docx Popgen Exercise <nowiki>[PDFDOCX]</nowiki>]* [http:// To run the exercise from docker image provided, <pre>statgen.us-setup login --tutorial popgen</files/tutorials/population/popgen_drift.q R Script for popgen_drift]pre>* [http://statgen.us/files/tutorials/population/popgen_selection.q R Script for popgen_selection]
==PSEQ==
* [httphttps://statgengithub.uscom/filesstatgenetics/tutorialsstatgen-courses/pseqblob/PSEQ_exercisemaster/handout/PSEQ.pdf PSEQ Exercise <nowiki>[PDF]</nowiki>]* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/PSEQ.ipynb PSEQ Exercise <nowiki>[Ipython Notebook]</nowiki>] To run the exercise from docker image provided, <pre>statgen-setup launch --tutorial pseq</pre> Notice that since PSEQ Commands exercise does not involve generating and visualizing plots, it is also fine to use a command terminal, instead of the JupyterLab server, to run this exercise and reproduce exactly what was described in the tutorial. To do so, <pre>statgen-setup login --tutorial pseq</pre> ==REGENIE==* [https://github.com/statgenetics/statgen-courses/blob/master/handout/regenie_example.pdf REGENIE Exercise|<nowiki>[PDF]</nowiki>]* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/regenie_example.ipynb REGENIE Exercise Commands<nowiki>[Ipython Notebook]</nowiki>] To run the exercise from docker image provided, <pre>statgen-setup launch --tutorial regenie</pre> Then follow prompts on the terminal output to open up the JupyterLab server in your web browser. If it is the first time you start this server, please open a command terminal inside JupyterLab, and type <pre>get-data</pre> to load the data-set to the JupyterLab workspace.
==Regression==
* [httphttps://statgengithub.uscom/statgenetics/statgen-courses/blob/filesmaster/tutorialshandout/regression_exerciseregression.pdf docx Regression Exercise <nowiki>[PDFDOCX]</nowiki>]
* [[Regression_Exercise|Exercise Commands]]
To install run the exercise from packagesdocker image provided, follow the configuration steps above and run the following command. <pre>statgen-setup login --tutorial regression</pre>
==RV-TDT==
* [httphttps://statgengithub.uscom/statgenetics/statgen-courses/filesblob/tutorialsmaster/rvtdthandout/rvtdt_exerciseRV-TDT.pdf doc Exercise <nowiki>[PDFDOC]</nowiki>]
* [[RV-TDT|Exercise Commands]]
==SLINK==
* [httphttps://statgengithub.uscom/statgenetics/statgen-courses/filesblob/tutorialsmaster/seqsparkhandout/slink_ex_shortSlink.pdf doc SLINK Exercise <nowiki>[PDFDOCX]</nowiki>]
To run the exercise from docker image provided,
==SUPERLINK==
==Variant Association Tools==
* [httphttps://statgengithub.uscom/filesstatgenetics/tutorialsstatgen-courses/VAT_exercise_2018_nographsblob/master/handout/VAT.pdf docx VAT Exercise <nowiki>[PDFDOCX]</nowiki>]* [[https://github.com/statgenetics/statgen-courses/blob/master/notebooks/VAT.ipynb VAT Commands in Exercise|Exercise Commands<nowiki>[Ipython notebook]</nowiki>]